Elementolab/
From Icbwiki
This is the wiki area of the Elemento Lab website.
- ChIPseeqer: A comprehensive framework for the analysis of ChIP-seq data
- Installation Instructions
- FAQ
- Versions
- Graphical User Interface version
- Command-line version
- LATEST NEWS
- [01/14/2013] New hg19 annotation files for ChIPseeqer. Download here.
- [12/03/2012] ChIPseeqer v2.1 is out! Check out the Installation Instructions.
- [07/23/2011] Our paper ChIPseeqer in BMC Bioinformatics 2011, 12:277 has been highlighted as
- [07/07/2011] The ChIPseeqer publication is out! An integrated ChIP-seq analysis platform with customizable workflows Eugenia G Giannopoulou and Olivier Elemento, BMC Bioinformatics 2011, 12:277.
- [06/22/2011] ChIPseeqer v2.0 known issues and how to address them.
- [05/23/2011] ChIPseeqer v2.0 is out! Check out the Installation Instructions.
- [02/17/2011] ChIPseeqer now available as a user-friendly graphical interface! Check out the Installation Instructions and Tutorial.
- [01/29/2011] Want to overlap your peaks with other ChIP-seq datasets from Encode? Use option --type=Encode and --TFname=select_TF in ChIPseeqerNongenicAnnotate to get the peaks overlap with a specific ChIP-seq dataset from ENCODE.
- Older news.
- 3D chromosome structure visualization
- Visualizing functional links among sequencing variants using VizVar
- SNVseeqer: Single Nucleotide Variant and mutation detection from RNA-seq and DNA-seq data
- GeneTools: the Elemento lab deep sequencing analysis toolbox
- RRBSeeqer: Analysis of DNA methylation data, using Reduced Representation Bisulfite Sequencing (RRB-seq).
Paper describing RRB-Seq: Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
- miRSeeqer: small RNA-seq analysis
- FIRE: Finding Informative Regulatory Elements
- Download at https://tavazoielab.c2b2.columbia.edu/FIRE/ or get it from our subversion repository : svn co https://pbtech-vc.med.cornell.edu/public/svn/elementolab/FIRE/trunk FIRE/ (restricted to ICB)
- Tutorial at https://tavazoielab.c2b2.columbia.edu/FIRE/tutorial.html
- Frequently Asked Questions about FIRE
- Fast Promoter Extraction
- iPAGE: Pathway Analysis of Gene Expression
- Primary download page with GUI, etc is http://tavazoielab.c2b2.columbia.edu/iPAGE
- Alternative download with ElementoLab-specific functions, databases, etc at http://physiology.med.cornell.edu/faculty/elemento/lab/files/PAGE.zip
- from our subversion repository (ICB): svn co https://pbtech-vc.med.cornell.edu/public/svn/elementolab/PAGE/trunk PAGE/ (restricted to ICB)
- from our subversion repository (everybody else): svn co --username=guest --password=email@email.com https://pbtech-vc.med.cornell.edu/public/svn/elementolab/PAGE/trunk PAGE/
- PAGE Tutorial
- Howto: add new pathway database to PAGE
- FIREpro: Ab initio discovery of protein regulatory motifs
- Resources
- Epiworkshop 2013
- Epiworkshop 2012
- Elemento lab participation in CSHL Summer School
- R tutorial
- Subversion Source Browser
- GenRegexp
- C/C++ Programming
- Perl tips
- Tutorial for various tools (clustering, etc)
- ICB/Elementolab Subversion tutorial
- Datasets
- Unix/Mac tips
- Deep Sequencing Resources
- Gene Identifiers
- Formats
- Elementolab/Peak Finding with Promoter Arrays
- Elementolab/PBM Motifs
- Tips on using the Panda computer cluster
- Compute genome mappability
- Web Application Design
- QT Tips
- Image analysis
- Database of Cancer Drug Resistance Mutations
- Computing RPKM values from RNA-seq data
- Big Data
- Data Visualization
- Social Media Howtos and Natural Language Processing
- Analysis Pipelines
- Funding
- Format changes for R01s http://grants.nih.gov/grants/guide/notice-files/NOT-OD-09-149.html
- Tips for revising an NIH grant http://scientopia.org/blogs/drugmonkey/2011/08/29/structural-aspects-of-revising-your-nih-grant/
- Documents http://grants.nih.gov/grants/funding/phs398/phs398.html
- Damon Runyon-Rachleff Innovation Award http://www.damonrunyon.org/for_scientists/more/innovation_award_overview
- Stand Up to Cancer http://www.aacr.org/home/public--media/stand-up-to-cancer/grant-giving-model-and-expert-review-process/su2c-innovative-research-grants.aspx
- Illumina IDEA challenge http://www.illumina.com/landing/idea/
- LLS TRP http://www.leukemia-lymphoma.org/all_page.adp?item_id=11620
- Microsoft Research Fellow http://research.microsoft.com/en-us/collaboration/awards/msrff_application.aspx
- Google Research Awards http://research.google.com/university/relations/research_awards.html (deadlines are usually April 15 and October 15)
- Sidney Kimmel Scholar (deadline Dec 1) http://www.kimmel.org/Application_Process37.html
- Human Frontiers (deadline ~ mid-March) http://www.hfsp.org/funding/research-grants/information-and-guidelines
- James McDonnell Foundation (deadline: March 15): http://www.jsmf.org/apply/research/index.htm
- Brain Tumor Foundation http://www.braintumor.org/research/funding-opportunities/
- United Against Lung Cancer http://www.unitingagainstlungcancer.org/research/programs/fundingopps (deadline Aug 12)
- American Cancer Society Research Grants http://www.cancer.org/research/researchprogramsfunding/fundingopportunities/indexofgrants/researchgrantsforindependentinvestigators/research-scholar-grants (deadline April 1 and Oct 1)
- Lungevity http://events.lungevity.org/site/PageServer?pagename=v2_Research_ApplicationDetails
- Working at Cornell
- J-1 Waiver rules http://www.isso.cornell.edu/academicstaff/jwaiver.php
- Events
- The Rockefeller Calendar of Events is the most comprehensive list of seminars in the tri-Inst area
- NextGen JC organized by Fabien
- Epigenomics meetings organized by Olivier
